Variant report

Variant	rs7647351
Chromosome Location	chr3:121422109-121422110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121420842..121422524-chr3:121426480..121428817,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10049060	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1127412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128163	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1169	0.83[CHB][hapmap]
rs11916169	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12496318	1.00[CEU][hapmap]
rs12634032	1.00[CEU][hapmap]
rs12635865	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1344279	0.93[CEU][hapmap]
rs1463736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1574115	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1574133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920297	1.00[CEU][hapmap]
rs1920298	1.00[CEU][hapmap]
rs1920299	1.00[CEU][hapmap]
rs2141487	1.00[CEU][hapmap]
rs2689285	1.00[CEU][hapmap]
rs2689290	0.93[CEU][hapmap]
rs3732407	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3732410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772126	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes]
rs4048699	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4048703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58367397	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771068	1.00[CEU][hapmap]
rs6791882	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610298	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7623901	1.00[CEU][hapmap]
rs7637495	1.00[CEU][hapmap]
rs7648340	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648343	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9808981	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9817818	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9818073	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9820511	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9824235	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824760	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9838301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9850439	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9852845	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9874722	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7647351	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs7647351	STAM2	trans	lymphoblastoid	RTeQTL
rs7647351	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs7647351	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs7647351	EAF2	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:121396800-121435600	Weak transcription	Psoas Muscle	Psoas
3	chr3:121399000-121425400	Weak transcription	Pancreas	Pancrea
4	chr3:121399000-121426400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:121399000-121440400	Weak transcription	K562	blood
6	chr3:121401200-121429400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:121401200-121434000	Weak transcription	Gastric	stomach
8	chr3:121404000-121432800	Weak transcription	Brain Angular Gyrus	brain
9	chr3:121407400-121429400	Weak transcription	Esophagus	oesophagus
10	chr3:121408200-121422400	Strong transcription	Placenta	Placenta
11	chr3:121408200-121428400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:121408600-121422800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:121408600-121424600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:121408600-121424800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:121408600-121424800	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr3:121408600-121427400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:121408600-121428200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr3:121408800-121422800	Strong transcription	Primary B cells from cord blood	blood
19	chr3:121408800-121424800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:121410400-121435600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:121410800-121424400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:121411000-121432000	Weak transcription	NHEK	skin
23	chr3:121411000-121432800	Weak transcription	Fetal Brain Male	brain
24	chr3:121411000-121442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:121411400-121432800	Weak transcription	Colonic Mucosa	Colon
26	chr3:121411400-121437200	Weak transcription	Small Intestine	intestine
27	chr3:121412200-121423200	Weak transcription	Fetal Intestine Small	intestine
28	chr3:121413400-121446200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:121414200-121428000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:121414600-121422400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:121414800-121436200	Weak transcription	Stomach Mucosa	stomach
32	chr3:121415200-121422600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr3:121415200-121422600	Strong transcription	Fetal Intestine Large	intestine
34	chr3:121415400-121424800	Strong transcription	Liver	Liver
35	chr3:121415400-121427400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:121415600-121428400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:121415800-121423200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr3:121416000-121425000	Strong transcription	Primary hematopoietic stem cells	blood
39	chr3:121416400-121423200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:121416400-121425200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:121417200-121424200	Weak transcription	Right Ventricle	heart
42	chr3:121417200-121430800	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:121417200-121435800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:121417400-121426200	Weak transcription	Thymus	Thymus
45	chr3:121417400-121431600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:121417600-121423200	Weak transcription	Fetal Stomach	stomach
47	chr3:121417600-121424200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:121417600-121425400	Weak transcription	Lung	lung
49	chr3:121417600-121430800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:121417600-121431600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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